Contacts of the helix formed by residues 206 - 214 (chain E) in PDB entry 6M04
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 206 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D LYS* 4.8 2.7 + - - -
202E LYS 5.0 4.7 - - - -
203E CYS 4.1 7.6 - - - -
204E PHE 3.4 3.8 - - - -
205E GLU* 1.3 77.3 - - - +
207E PRO* 1.3 64.5 - - - +
208E TRP* 3.6 15.9 + - - +
209E THR* 2.4 47.6 + - - +
210E THR 4.0 0.2 + - - -
280E ASP* 5.5 1.2 - - - +
284E ALA* 4.5 8.8 - - - +
287E LEU* 5.4 4.9 - - - -
433E ARG* 3.2 1.6 + - - +
437E PHE* 4.4 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 207 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA* 4.5 22.0 - - + -
289D GLU* 5.1 0.3 - - - +
290D LYS* 5.5 4.7 - - - -
205E GLU 3.3 9.4 - - - +
206E SER* 1.3 83.3 - - - +
208E TRP* 1.3 61.2 + - - +
209E THR 3.2 0.2 - - - -
210E THR* 3.3 15.1 - - + +
211E LYS* 3.0 26.6 + - - +
280E ASP* 4.6 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E SER* 3.2 8.4 - - - +
207E PRO* 1.3 83.1 - - - +
209E THR* 1.3 60.7 + - + +
211E LYS* 3.2 28.7 + - + +
212E ALA* 2.8 40.6 + - + +
215E GLU* 5.7 1.0 + - - -
280E ASP* 4.1 21.1 + - + +
284E ALA* 4.4 4.9 - - + -
288E PHE* 3.5 23.6 - + - -
436E VAL* 4.6 5.6 - - + -
437E PHE* 3.5 25.8 - + - -
442E SER* 3.1 47.1 - - - -
445E LYS* 4.5 8.2 - - + +
446E LEU* 3.4 43.4 - - + +
449E ILE* 6.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 209 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D LYS* 5.0 0.7 + - - -
293D LYS* 5.6 1.0 + - - -
206E SER* 2.4 28.7 + - - +
208E TRP* 1.3 82.1 - - + +
210E THR* 1.3 64.7 + - - +
212E ALA* 3.3 2.8 + - - +
213E LEU* 2.9 38.2 + - - +
433E ARG* 2.5 39.3 + - - +
436E VAL* 5.2 8.5 - - + -
437E PHE* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA* 5.5 2.7 - - - +
289D GLU* 2.8 57.9 + - + +
290D LYS* 4.9 17.9 - - + -
293D LYS* 4.6 23.1 - - - +
207E PRO* 3.3 24.2 - - + +
209E THR* 1.3 82.1 + - - +
211E LYS* 1.3 60.3 + - - +
213E LEU* 4.2 8.0 - - - +
214E SER* 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D GLU* 4.2 6.3 - - - +
478D MET* 6.6 0.4 - - + -
207E PRO 3.0 18.1 + - - +
208E TRP* 3.2 26.5 + - - +
210E THR* 1.3 78.1 - - - +
212E ALA* 1.3 57.1 + - - +
214E SER* 3.4 12.0 + - - +
215E GLU* 3.3 23.8 - - - +
277E ASP* 3.7 25.0 + - - +
280E ASP* 3.5 21.9 + - - +
446E LEU* 5.6 0.8 - - - +
449E ILE* 5.4 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E TRP* 2.8 44.9 + - + +
209E THR* 3.6 3.6 - - - +
211E LYS* 1.3 75.2 - - - +
213E LEU* 1.3 68.1 + - + +
215E GLU* 3.7 16.1 - - - +
216E THR* 3.5 19.8 + - - +
409E ILE* 5.4 5.0 - - - +
436E VAL* 5.8 0.9 - - + -
442E SER* 4.7 6.1 - - - +
445E LYS* 6.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D LYS* 6.3 0.7 - - - +
209E THR* 2.9 25.0 + - - +
210E THR* 3.4 8.5 + - - +
212E ALA* 1.3 80.6 - - + +
214E SER* 1.3 57.2 + - - +
215E GLU 3.2 5.2 - - - -
216E THR 3.2 19.2 - - - +
407E SER* 3.3 27.4 - - - +
409E ILE* 5.3 7.4 - - + -
432E LYS* 5.7 7.0 - - + -
436E VAL* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D GLU* 3.0 21.0 + - - -
210E THR* 2.9 17.0 + - - -
211E LYS* 3.4 9.7 + - - +
213E LEU* 1.3 74.8 - - - +
215E GLU* 1.3 58.2 + - - +
216E THR 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il